[gmx-users] Unreadable trajetory

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 14 13:18:53 CET 2012

On 14/03/2012 5:59 PM, Jernej Zidar wrote:
> Hi.
>    I'm testing a forcefield with a combination of CPT and NVT MD
> simulations of a polymer in water. I adopted the equilibration steps
> form the CHARMM equilibration steps:
> 1. Fix solute (using "define  = -DPOSRES" ).
> a) 10.000 steps of steepest descent minimization
> b) 10.000 steps of conjugated gradient minimization with a steepest
> descents every 1000 steps
> c) 100.000 steps of NVT MD during which I slowly heat the system to 300 K
> d) 100.000 steps of CPT MD
> e) 100.000 steps of NVT MD
> f) 100.000 steps of CPT MD
> g) 100.000 steps of NVT MD
> h) 100.000 steps of CPT MD

Writing 100,000 or 100.000 for 100000 is prone to misinterpretation. Get 
out of the habit of using a thousands separator in scientific contexts :-)

> 2. Remove contraints and repeat steps a-h.
>    The problem I'm having is that I cannot visualize the trajectories
> from step 2.e) onwards with VMD simply segfaulting. While it may well
> be a VMD issue but I can't visualize the trajectory using ngmx (blank
> screen) either, so it's an issue either with my inputs or Gromacs.

Your .mdp file is not writing any trajectory frames.


>    I tried to use trjconv tool to adjust the centering or remove the
> PBC or save just the polymer residues but the utility always fails
> with: WARNING no output, last frame read at t=200.
>    Checking the run log file did not reveal any errors. Checking the
> EDR file revealed no jumps in any of the enery terms.
>    What's most surprising, is that I can visualize the GRO file that is
> generated at the end of the simulation.
>    The relevant files are on the following links:
> - MDP: http://dl.dropbox.com/u/5761806/md-nvt-2-nofix.mdp
> - LOG: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.log
> - TPR: http://dl.dropbox.com/u/5761806/wpoly-2x-box-ions-nvt-nofix-2.tpr
>     I use GROMACS 4.5.5, the system is electrically neutral. To prepare
> a new TPR file a use the GRO file from the previous run.

Don't, you're losing precision and introducing perturbations. grompp -t 
old.cpt is your friend.


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